When you click on a file to download, the download starts right away, even though you still haven't selected the location. Then, after you select a location, Vivaldi moves the download to the location you've selected. But before you make a selection, Vivaldi will use the default download location for the temporary transmission.

Try opening Vivaldi Settings [alt+P] and searching for 'Download'. You'll see a setting for the default download location, which is '$HOME/Downloads'. Try changing that to any other location on your computer, and you should be fine.

Yes, that solves this for me, I meant this post more like a bug since I consider it impolite for any program to create its own directories in such a prominent location as my home folder without asking me to (opera 12 used a .tmp folder for this I think)